rnasa

Gene Expression Analyzer for RNA-seq samples

Installation

$ pip install -U https://github.com/dceoy/rnasa/archive/main.tar.gz

Dependent commands:

• pigz
• pbzip2
• bgzip
• samtools
• java
• fastqc
• trim_galore
• STAR
• rsem-refseq-extract-primary-assembly
• rsem-prepare-reference
• rsem-calculate-expression

Docker image

Pull the image from Docker Hub.

$ docker image pull dceoy/rnasa

Usage

1. Download and process resource data.

   $ rnasa download --genome=GRCh38 --dest-dir=/path/to/ref
   

2. Run the pipeline for gene expression analysis.

   $ rnasa run \
       --workers=2 \
       --dest-dir=. \
       /path/to/ref/GRCh38 \
       /path/to/sample1_fastq_prefix \
       /path/to/sample2_fastq_prefix \
       /path/to/sample3_fastq_prefix
   

   The command search for one (single-end) or two (paired-end) input FASTQ files by prefix.

Run rnasa --help for more information.